[Bioc-devel] file 'HilbertCurve/DESCRIPTION' does not exist

[Henrik Bengtsson]

The content of the .Rbuildignore file should be regular expression,
i.e. it does _not_ used fixed strings or globbing to match files and
folders. From 'Writing R Extensions': "To exclude files from being put
into the package, one can specify a list of exclude patterns in file
.Rbuildignore in the top-level source directory. These patterns should
be Perl-like regular expressions (see the help for regexp in R for the
precise details), one per line, to be matched case-insensitively
against the file and directory names relative to the top-level package
source directory."

In regular expression terms, '.o' matches any path that comprise a 'o'
(or 'O' because it's case-insensitive) preceded by any symbol. In
other words, 'DESCRIPTION' is matched because of the 'IO' part of it.
There are other files in this package that are dropped as well by the
'.o' exclusion, e.g.

$ ls -R -1 R/ | grep -i -E ".o"
00_S4_generic_methods.R
GenomicHilbertCurve.R
hc_polygon.R
RcppExports.R

There are probably other files in other subfolders that are dropped as well.

The proper way to exclude files with file extensions *.o and *.so via
.Rbuildignore is:

[.]o$
[.]so$

/Henrik

On Tue, Oct 8, 2024 at 7:22 AM Jennifer Wokaty
<Jennifer.Wokaty using sph.cuny.edu> wrote:
>
> Hi Zuguang,
>
> Sorry for the delayed response. `R CMD build` seems to have a problem with the second to last line of your .Rbuildignore, which had ".o". I'm not sure why but you could try substituting something else in its place to target your .o files, such as src/.o, in your .Rbuildignore to get it building again.
>
>
> Jennifer Wokaty (they/them)
>
> Waldron Lab at CUNY SPH
> Bioconductor Core Team
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Zuguang Gu <jokergoo using gmail.com>
> Sent: Tuesday, September 24, 2024 4:25 AM
> To: bioc-devel <bioc-devel using r-project.org>
> Subject: [Bioc-devel] file 'HilbertCurve/DESCRIPTION' does not exist
>
> * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. *
>
> Dear Bioc,
>
> I have been seeing this error from the HilbertCurve package (devel):
>
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FHilbertCurve%2F__%3B!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8jgvQQvo%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7Cbbb869428c8245ea230f08dcdc72824f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638627631609247752%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=hHY%2B%2FwUZlGBvqmh381GvG9jnOjuAywGbzFIDA8lkHRA%3D&reserved=0<https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/HilbertCurve/__;!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8jgvQQvo$>
>
> * checking for file ‘HilbertCurve/DESCRIPTION’ ... OK
> * preparing ‘HilbertCurve’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> * creating vignettes ... OK
> * cleaning src
> Error in .read_description(ldpath) :
>   file 'HilbertCurve/DESCRIPTION' does not exist
> Execution halted
>
> I've checked, the DESCRIPTION file is not missing. See the git commit
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fcode.bioconductor.org%2Fbrowse%2FHilbertCurve%2F728edd7e4b127bea4144ddce608602331817153b%2F__%3B!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8dJcAsaA%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7Cbbb869428c8245ea230f08dcdc72824f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638627631609268861%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=RM1CuicK1eGZnzU5Ky%2BCvs06ycCRcrAOCJnza2w%2Bjnw%3D&reserved=0<https://urldefense.com/v3/__https://code.bioconductor.org/browse/HilbertCurve/728edd7e4b127bea4144ddce608602331817153b/__;!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8dJcAsaA$>
> which was checked on bioc.
>
> Also the first line "checking for file ‘HilbertCurve/DESCRIPTION’ ... OK"
> already means the DESCRIPTION file does exist.
>
> Thanks!
> Zuguang Gu
>
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>
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